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Auger N, Douet-Guilbert N, Quessada J, Theisen O, Lafage-Pochitaloff M, Troadec MB. Cytogenetics in the management of myelodysplastic neoplasms (myelodysplastic syndromes, MDS): Guidelines from the groupe francophone de cytogénétique hématologique (GFCH). Curr Res Transl Med 2023; 71:103409. [PMID: 38091642 DOI: 10.1016/j.retram.2023.103409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 12/26/2023]
Abstract
Myelodysplastic neoplasms (MDS) are clonal hematopoietic neoplasms. Chromosomal abnormalities (CAs) are detected in 40-45% of de novo MDS and up to 80% of post-cytotoxic therapy MDS (MDS-pCT). Lately, several changes appeared in World Health Organization (WHO) classification and International Consensus Classification (ICC). The novel 'biallelic TP53 inactivation' (also called 'multi-hit TP53') MDS entity requires systematic investigation of TP53 locus (17p13.1). The ICC maintains CA allowing the diagnosis of MDS without dysplasia (del(5q), del(7q), -7 and complex karyotype). Deletion 5q is the only CA, still representing a low blast class of its own, if isolated or associated with one additional CA other than -7 or del(7q) and without multi-hit TP53. It represents one of the most frequent aberrations in adults' MDS, with chromosome 7 aberrations, and trisomy 8. Conversely, translocations are rarer in MDS. In children, del(5q) is very rare while -7 and del(7q) are predominant. Identification of a germline predisposition is key in childhood MDS. Aberrations of chromosomes 5, 7 and 17 are the most frequent in MDS-pCT, grouped in complex karyotypes. Despite the ever-increasing importance of molecular features, cytogenetics remains a major part of diagnosis and prognosis. In 2022, a molecular international prognostic score (IPSS-M) was proposed, combining the prognostic value of mutated genes to the previous scoring parameters (IPSS-R) including cytogenetics, still essential. A karyotype on bone marrow remains mandatory at diagnosis of MDS with complementary molecular analyses now required. Analyses with FISH or other technologies providing similar information can be necessary to complete and help in case of karyotype failure, for doubtful CA, for clonality assessment, and for detection of TP53 deletion to assess TP53 biallelic alterations.
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Affiliation(s)
- Nathalie Auger
- Gustave Roussy, Génétique des tumeurs, 144 rue Edouard Vaillant, Villejuif 94805, France
| | - Nathalie Douet-Guilbert
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France
| | - Julie Quessada
- Laboratoire de Cytogénétique Hématologique, CHU Timone Aix Marseille University, Marseille, France
| | - Olivier Theisen
- Hematology Biology, Nantes University Hospital, Nantes, France
| | | | - Marie-Bérengère Troadec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest F-29200, France; CHRU Brest, Laboratoire de Génétique Chromosomique, Service de génétique, Brest, France.
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2
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Loacker L, Petzer V, Bachmann S, Griesmacher A, Wolf D, Stauder R. High concordance of clone detection between peripheral blood and bone marrow by targeted next-generation sequencing-A pilot study in patients with MDS. Br J Haematol 2023; 202:e16-e19. [PMID: 37263977 DOI: 10.1111/bjh.18889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Affiliation(s)
- Lorin Loacker
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck Medical University Hospital, Innsbruck, Austria
| | - Verena Petzer
- Department of Internal Medicine V (Haematology and Oncology), Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Bachmann
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck Medical University Hospital, Innsbruck, Austria
| | - Andrea Griesmacher
- Central Institute for Medical and Chemical Laboratory Diagnosis, Innsbruck Medical University Hospital, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V (Haematology and Oncology), Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
| | - Reinhard Stauder
- Department of Internal Medicine V (Haematology and Oncology), Comprehensive Cancer Center Innsbruck (CCCI), Medical University of Innsbruck, Innsbruck, Austria
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3
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Tsekoura G, Agathangelidis A, Kontandreopoulou CN, Taliouraki A, Mporonikola G, Stavropoulou M, Diamantopoulos PT, Viniou NA, Aleporou V, Papassideri I, Kollia P. Deregulation of Autophagy and Apoptosis in Patients with Myelodysplastic Syndromes: Implications for Disease Development and Progression. Curr Issues Mol Biol 2023; 45:4135-4150. [PMID: 37232732 PMCID: PMC10217762 DOI: 10.3390/cimb45050263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
(1) Background: Myelodysplastic neoplasms (MDSs) consist of a group of blood malignancies with a complex biological background. In this context, we investigated the role of autophagy and apoptosis in the pathogenesis and progression of MDSs. (2) Methods: To address this issue, we performed a systematic expression analysis on a total of 84 genes in patients with different types of MDSs (low/high risk of malignancy) versus healthy individuals. Furthermore, real-time quantitative PCR (qRT-PCR) was used to validate significantly upregulated or downregulated genes in a separate cohort of MDS patients and healthy controls. (3) Results: MDS patients were characterized by lower expression levels for a large series of genes involved in both processes compared to healthy individuals. Of importance, deregulation was more pronounced in patients with higher-risk MDS. Results from the qRT-PCR experiments displayed a high level of concordance with the PCR array, strengthening the relevance of our findings. (4) Conclusions: Our results indicate a clear effect of autophagy and apoptosis on MDS development, which becomes more pronounced as the disease progresses. The results from the present study are expected to assist in our understanding of the biological background of MDSs as well as in the identification of novel therapeutic targets.
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Affiliation(s)
- Georgia Tsekoura
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Andreas Agathangelidis
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Angeliki Taliouraki
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Georgia Mporonikola
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Maria Stavropoulou
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Panagiotis T. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vassiliki Aleporou
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
| | - Issidora Papassideri
- Division of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece
| | - Panagoula Kollia
- Division of Genetics & Biotechnology, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece; (G.T.); (A.A.)
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4
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Træden D, Tulstrup M, Cowland JB, Sjö LD, Bøgsted M, Grønbæk K, Andersen MK, Hansen JW. A predictive model for bone marrow disease in cytopenia based on noninvasive procedures. Blood Adv 2022; 6:3541-3550. [PMID: 35427424 PMCID: PMC9198925 DOI: 10.1182/bloodadvances.2021006649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Bone marrow specimens are the core of the diagnostic workup of patients with cytopenia. To explore whether next-generation sequencing (NGS) could be used to rule out malignancy without bone marrow specimens, we incorporated NGS in a model to predict presence of disease in the bone marrow of patients with unexplained cytopenia. We analyzed the occurrence of mutations in 508 patients with cytopenia, referred for primary workup of a suspected hematologic malignancy from 2015 to 2020. We divided patients into a discovery (n = 340) and validation (n = 168) cohort. Targeted sequencing, bone marrow biopsy, and complete blood count were performed in all patients. Mutations were identified in 267 (53%) and abnormal bone marrow morphology in 188 (37%) patients. Patients with isolated neutropenia had the lowest frequency of both mutations (21%) and abnormal bone marrow morphology (5%). The median number of mutations per patient was 2 in patients with abnormal bone marrow morphology compared with 0 in patients with a nondiagnostic bone marrow morphology (P < .001). In a multivariable logistic regression, mutations in TET2, SF3B1, U2AF1, TP53, and RUNX1 were significantly associated with abnormal bone marrow morphology. In the validation cohort, a model combining mutational status and clinical data identified 34 patients (20%) without abnormal bone marrow morphology with a sensitivity of 100% (95% confidence interval: 93%-100%). Overall, we show that NGS combined with clinical data can predict the presence of abnormal bone marrow morphology in patients with unexplained cytopenia and thus can be used to assess the need of a bone marrow biopsy.
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Affiliation(s)
- Dicte Træden
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Tulstrup
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Martin Bøgsted
- Department of Hematology, Aalborg University Hospital, Aalborg, Denmark; and
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Jakob Werner Hansen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Spitzer B, Rutherford KD, Gundem G, McGovern EM, Millard NE, Arango Ossa JE, Cheung IY, Gao T, Levine MF, Zhang Y, Medina-Martínez JS, Feng Y, Ptashkin RN, Bolton KL, Farnoud N, Zhou Y, Patel MA, Asimomitis G, Cobbs CC, Mohibullah N, Huberman KH, Arcilla ME, Kushner BH, Modak S, Kung AL, Zehir A, Levine RL, Armstrong SA, Cheung NKV, Papaemmanuil E. Bone Marrow Surveillance of Pediatric Cancer Survivors Identifies Clones that Predict Therapy-Related Leukemia. Clin Cancer Res 2022; 28:1614-1627. [PMID: 35078859 PMCID: PMC9983778 DOI: 10.1158/1078-0432.ccr-21-2451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/01/2021] [Accepted: 01/20/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Therapy-related myelodysplastic syndrome and acute leukemias (t-MDS/AL) are a major cause of nonrelapse mortality among pediatric cancer survivors. Although the presence of clonal hematopoiesis (CH) in adult patients at cancer diagnosis has been implicated in t-MDS/AL, there is limited published literature describing t-MDS/AL development in children. EXPERIMENTAL DESIGN We performed molecular characterization of 199 serial bone marrow samples from 52 patients treated for high-risk neuroblastoma, including 17 with t-MDS/AL (transformation), 14 with transient cytogenetic abnormalities (transient), and 21 without t-MDS/AL or cytogenetic alterations (neuroblastoma-treated control). We also evaluated for CH in a cohort of 657 pediatric patients with solid tumor. RESULTS We detected at least one disease-defining alteration in all cases at t-MDS/AL diagnosis, most commonly TP53 mutations and KMT2A rearrangements, including involving two novel partner genes (PRDM10 and DDX6). Backtracking studies identified at least one t-MDS/AL-associated mutation in 13 of 17 patients at a median of 15 months before t-MDS/AL diagnosis (range, 1.3-32.4). In comparison, acquired mutations were infrequent in the transient and control groups (4/14 and 1/21, respectively). The relative risk for development of t-MDS/AL in the presence of an oncogenic mutation was 8.8 for transformation patients compared with transient. Unlike CH in adult oncology patients, TP53 mutations were only detectable after initiation of cancer therapy. Last, only 1% of pediatric patients with solid tumor evaluated had CH involving myeloid genes. CONCLUSIONS These findings demonstrate the clinical relevance of identifying molecular abnormalities in predicting development of t-MDS/AL and should guide the formation of intervention protocols to prevent this complication in high-risk pediatric patients.
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Affiliation(s)
- Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
- Department of Pediatrics, Weill Cornell Medical College, New York, NY
| | - Kayleigh D. Rutherford
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunes Gundem
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin M. McGovern
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan E. Millard
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA
| | - Juan E. Arango Ossa
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Irene Y. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Teng Gao
- Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA
| | - Max F. Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan S. Medina-Martínez
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelly L. Bolton
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO
| | - Noushin Farnoud
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yangyu Zhou
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Minal A. Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Georgios Asimomitis
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cassidy C. Cobbs
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neeman Mohibullah
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kety H. Huberman
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria E. Arcilla
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian H. Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Human Oncology and Oncogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Scott A. Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Nai Kong V. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Elli Papaemmanuil
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
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6
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Concordance of Peripheral Blood and Bone Marrow Next-Generation Sequencing in Hematologic Neoplasms. Adv Hematol 2022; 2022:8091746. [PMID: 35378848 PMCID: PMC8976630 DOI: 10.1155/2022/8091746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Objective. Mutational analysis by next-generation sequencing (NGS) obtained by peripheral blood NGS has been of clinical interest to use as a minimally invasive screening tool. Our study evaluates the correlation between NGS results on peripheral blood and bone marrow in hematolymphoid disease. Method. We evaluated patients who had NGS for presumed hematologic malignancy performed on peripheral blood and bone marrow within a 1-year interval of each other. We excluded cases in which chemotherapy or bone marrow transplant occurred in the interval between the two tests. The concordance across peripheral blood and bone marrow NGS results was assessed by kappa coefficient analysis. Results. A total of 163 patients were studied. Concordance of peripheral blood and bone marrow NGS found in 150 patients (92.0%) with a kappa coefficient of 0.794 (kappa standard error 0.054) and
value for testing kappa <0.0001. Myeloid neoplasms showed concordant results in 77/78 cases (98.7%) with a kappa coefficient of 0.916. Lymphoid neoplasms showed concordant results in 26/31 cases (83.9%) with a kappa coefficient of 0.599. Nonneoplastic cases showed concordant results in 47/54 cases (87.0%) with a kappa coefficient of 0.743. Conclusion. Peripheral blood NGS is a reliable tool for mutational analysis and provides a less invasive method for screening and monitoring of the molecular profile.
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7
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Wang W, Auer P, Zhang T, Spellman S, Carlson KS, Nazha A, Bolon YT, Saber W. Impact of Epigenomic Hypermethylation at TP53 on Allogeneic Hematopoietic Cell Transplantation Outcomes for Myelodysplastic Syndromes. Transplant Cell Ther 2021; 27:659.e1-659.e6. [PMID: 33992829 PMCID: PMC8421055 DOI: 10.1016/j.jtct.2021.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/03/2021] [Accepted: 04/29/2021] [Indexed: 01/25/2023]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell disorders for which allogeneic hematopoietic cell transplantation (HCT) is currently the sole curative treatment. Epigenetic lesions are considered a major pathogenetic determinant in many cancers, and in MDS, epigenetic-based interventions have emerged as life-prolonging therapies. However, the impact of epigenomic aberrations on HCT outcomes among patients with MDS are not well understood. We hypothesized that epigenomic signatures in MDS patients before undergoing HCT serve as a novel prognostic indicator of the risk of post-HCT MDS relapse. To evaluate these epigenomic signatures in MDS patients, we analyzed reduced representation bisulfite sequencing profiles in a matched case-control population of 94 patients. Among these HCT recipients, 47 patients with MDS who relapsed post-HCT (cases) were matched 1:1 to patients with MDS who did not relapse (controls). Only patients with wild-type TP53, RAS pathway, and JAK2 mutations were included in this study to promote the discovery of novel factors. Cases were matched with controls based on conditioning regimen intensity, age, sex, Revised International Prognostic Scoring System, Karnofsky Performance Status, graft type, and donor type. Pre-HCT whole-blood samples from cases and matched controls were obtained from the Center for International Blood and Marrow Transplant Research repository. We comprehensively identified differentially methylated regions (DMRs) by comparing the methylation patterns among matched cases and controls. Our findings show that cases displayed more hyper-DMRs pretransplantation compared with controls, even after adjusting for pre-HCT use of hypomethylating agents. Hyper-DMRs specific to cases were mapped to the transcription start site of 218 unique genes enriched in 5 different signaling pathways that may serve as regions of interest and factors to consider as prognostic determinants of post-HCT relapse in MDS patients. Interestingly, although patients selected for this cohort were wild-type for the TP53 gene, cases showed significantly greater levels of methylation at TP53 compared with controls. These findings indicate that previously identified prognostic genes for MDS, such as TP53, may affect disease relapse not only through genetic mutation, but also through epigenetic methylation mechanisms.
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Affiliation(s)
- Wei Wang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Paul Auer
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota
| | - Tao Zhang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | | | - Aziz Nazha
- Leukemia Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Avon Lake, Ohio
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota.
| | - Wael Saber
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
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8
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Kawata E, Lazo-Langner A, Xenocostas A, Hsia CC, Howson-Jan K, Deotare U, Saini L, Yang P, Broadbent R, Levy M, Howlett C, Stuart A, Kerkhof J, Santos S, Lin H, Sadikovic B, Chin-Yee I. Clinical value of next-generation sequencing compared to cytogenetics in patients with suspected myelodysplastic syndrome. Br J Haematol 2020; 192:729-736. [PMID: 32588428 DOI: 10.1111/bjh.16891] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing (NGS) increasingly influences diagnosis, prognosis and management of myelodysplastic syndrome (MDS). In addition to marrow morphology and flow cytometry, our institution performs cytogenetics (CG) and NGS-based testing routinely in patients with suspected MDS. We evaluated the relative value of NGS in the assessment of patients with suspected MDS. We initially compared the diagnostic and prognostic information derived from CG and NGS in 134 patients. NGS enhanced the diagnostic yield compared to CG for clonal myeloid disorders (sensitivity 77% vs. 42·2%; specificity 90·2% vs. 78%; positive predictive value 92·8% vs. 76%; and negative predictive value 70·8% vs. 45·5%). The identification of poor prognosis mutations by NGS altered risk category in 27/39 (69·2%) patients with MDS with good/intermediate risk CG. Subsequently, we prospectively evaluated 70 patients with suspected MDS using an 'NGS-first approach' with CG restricted to samples with morphological abnormalities. We rarely identified mutations or CG abnormalities in patients without dysplastic features. NGS has a superior diagnostic performance compared to CG in patients with suspected MDS. We estimate that by using an 'NGS-first approach' we could reduce karyotyping by approximately 30%.
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Affiliation(s)
- Eri Kawata
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Department of Hematology, Matsushita Memorial Hospital, Moriguchi, Osaka, Japan.,Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan
| | - Alejandro Lazo-Langner
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Anargyros Xenocostas
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Cyrus C Hsia
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Kang Howson-Jan
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Uday Deotare
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Lalit Saini
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ping Yang
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Cytogenetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Robert Broadbent
- Cytogenetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Christopher Howlett
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Alan Stuart
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Hanxin Lin
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, London Health Sciences Centre, London, Ontario, Canada
| | - Ian Chin-Yee
- Division of Hematology, Department of Medicine, London Health Sciences Centre, London, Ontario, Canada.,Division of Hematology, Department of Medicine, Schulish School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Pathology & Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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9
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Clinical utility of targeted next-generation sequencing–based screening of peripheral blood in the evaluation of cytopenias. Blood 2019; 134:2222-2225. [DOI: 10.1182/blood.2019001610] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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10
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Diagnosis and Treatment of Chronic Myelomonocytic Leukemias in Adults: Recommendations From the European Hematology Association and the European LeukemiaNet. Hemasphere 2018; 2:e150. [PMID: 31723789 PMCID: PMC6745959 DOI: 10.1097/hs9.0000000000000150] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/11/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic myelomonocytic leukemia (CMML) is a disease of the elderly, and by far the most frequent overlap myelodysplastic/myeloproliferative neoplasm in adults. Aside from the chronic monocytosis that remains the cornerstone of its diagnosis, the clinical presentation of CMML includes dysplastic features, cytopenias, excess of blasts, or myeloproliferative features including high white blood cell count or splenomegaly. Prognosis is variable, with several prognostic scoring systems reported in recent years, and treatment is poorly defined, with options ranging from watchful waiting to allogeneic stem cell transplantation, which remains the only curative therapy for CMML. Here, we present on behalf of the European Hematology Association and the European LeukemiaNet, evidence- and consensus-based guidelines, established by an international group of experts, from Europe and the United States, for standardized diagnostic and prognostic procedures and for an appropriate choice of therapeutic interventions in adult patients with CMML.
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11
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Diagnostic algorithm for lower-risk myelodysplastic syndromes. Leukemia 2018; 32:1679-1696. [PMID: 29946191 DOI: 10.1038/s41375-018-0173-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/20/2018] [Accepted: 04/05/2018] [Indexed: 01/01/2023]
Abstract
Rapid advances over the past decade have uncovered the heterogeneous genomic and immunologic landscape of myelodysplastic syndromes (MDS). This has led to notable improvements in the accuracy and timing of diagnosis and prognostication of MDS, as well as the identification of possible novel targets for therapeutic intervention. For the practicing clinician, however, this increase in genomic, epigenomic, and immunologic knowledge needs consideration in a "real-world" context to aid diagnostic specificity. Although the 2016 revision to the World Health Organization classification for MDS is comprehensive and timely, certain limitations still exist for day-to-day clinical practice. In this review, we describe an up-to-date diagnostic approach to patients with suspected lower-risk MDS, including hypoplastic MDS, and demonstrate the requirement for an "integrated" diagnostic approach. Moreover, in the era of rapid access to massive parallel sequencing platforms for mutational screening, we suggest which patients should undergo such analyses, when such screening should be performed, and how those data should be interpreted. This is particularly relevant given the recent findings describing age-related clonal hematopoiesis.
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12
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Asadi Fakhr Z, Mehrzad V, Izaditabar A, Salehi M. Evaluation of the utility of peripheral blood vs bone marrow in karyotype and fluorescence in situ hybridization for myelodysplastic syndrome diagnosis. J Clin Lab Anal 2018; 32:e22586. [PMID: 29893006 DOI: 10.1002/jcla.22586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/19/2018] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE To clear the role of peripheral blood as a substitution for bone marrow in myelodysplastic syndrome and to evaluate the concordance between peripheral blood and bone marrow using karyotype and fluorescence in situ hybridization (FISH) methods. METHODS We examined 35 bone marrow (BM) and peripheral blood (PB) samples from myelodysplastic syndrome (MDS) patient using karyotype and FISH. Karyotype method for BM and PB samples performed using the standard protocol with an exception for peripheral blood in which growth factor for cultivation was not used. FISH testing was performed using a panel of MDS-associated probes to detect 20q12, 20qter, 5q31, 5q33, 5p15 and chromosome 7 and 8 centromeres. RESULTS Our results showed karyotypes of BM and PB are concordant in 74% of cases, while about 53% of these concordances were achieved from cases with normal karyotypes. However, the results of BM FISH were completely concordant with PB FISH. CONCLUSION Although peripheral blood karyotype is not trustworthy for MDS diagnosis, examining peripheral blood, using the FISH method, could be useful for clinical monitoring.
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Affiliation(s)
- Zhaleh Asadi Fakhr
- Department of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Science, Isfahan, Iran
| | - Valiollah Mehrzad
- Department of Hematology and Oncology, Medical School, Omid Hospital, Isfahan University of Medical Science, Isfahan, Iran
| | | | - Mansoor Salehi
- Department of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Science, Isfahan, Iran.,Medical Genetics Center of Genome, Isfahan, Iran
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13
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Duchmann M, Yalniz FF, Sanna A, Sallman D, Coombs CC, Renneville A, Kosmider O, Braun T, Platzbecker U, Willems L, Adès L, Fontenay M, Rampal R, Padron E, Droin N, Preudhomme C, Santini V, Patnaik MM, Fenaux P, Solary E, Itzykson R. Prognostic Role of Gene Mutations in Chronic Myelomonocytic Leukemia Patients Treated With Hypomethylating Agents. EBioMedicine 2018; 31:174-181. [PMID: 29728305 PMCID: PMC6013781 DOI: 10.1016/j.ebiom.2018.04.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 04/20/2018] [Indexed: 12/02/2022] Open
Abstract
Somatic mutations contribute to the heterogeneous prognosis of chronic myelomonocytic leukemia (CMML). Hypomethylating agents (HMAs) are active in CMML, but analyses of small series failed to identify mutations predicting response or survival. We analyzed a retrospective multi-center cohort of 174 CMML patients treated with a median of 7 cycles of azacitidine (n = 68) or decitabine (n = 106). Sequencing data before treatment initiation were available for all patients, from Sanger (n = 68) or next generation (n = 106) sequencing. Overall response rate (ORR) was 52%, including complete response (CR) in 28 patients (17%). In multivariate analysis, ASXL1 mutations predicted a lower ORR (Odds Ratio [OR] = 0.85, p = 0.037), whereas TET2mut/ASXL1wt genotype predicted a higher CR rate (OR = 1.18, p = 0.011) independently of clinical parameters. With a median follow-up of 36.7 months, overall survival (OS) was 23.0 months. In multivariate analysis, RUNX1mut (Hazard Ratio [HR] = 2.00, p = .011), CBLmut (HR = 1.90, p = 0.03) genotypes and higher WBC (log10(WBC) HR = 2.30, p = .005) independently predicted worse OS while the TET2mut/ASXL1wt predicted better OS (HR = 0.60, p = 0.05). CMML-specific scores CPSS and GFM had limited predictive power. Our results stress the need for robust biomarkers of HMA activity in CMML and for novel treatment strategies in patients with myeloproliferative features and RUNX1 mutations. TET2mut/ASXL1wt genotype predicts higher complete response rate and prolonged survival in CMML with hypomethylating agents. Conversely, RUNX1mut and CBLmut genotypes are associated with poorer outcome, independently of higher leukocyte count. CPSS and GFM prognostic scores showed modest performance when calculated at initiation of hypomethylating agents.
Somatic mutations contribute to the heterogeneous prognosis of chronic myelomonocytic leukemia (CMML). Hypomethylating agents (HMAs) are active in CMML. Response and survival in MDS and AML patients treated with HMAs is difficult to predict. We explore the predictive role of recurrent somatic mutations in a large retrospective cohort of 174 HMA-treated CMMLs. Consistent with MDS studies, we report a higher response rate in TET2mut/ASXL1wt patients. We also identify a CMML-specific molecular pattern (RUNX1mut or CBLmut) associated with shorter survival. Our results can inform treatment decision in CMML, for instance by using HMAs prior to transplant in TET2mut/ASXL1wt patients.
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Affiliation(s)
| | | | - Alessandro Sanna
- MDS Unit-Hematology, Università di Firenze AOU careggi, Firenze, Italy
| | - David Sallman
- Malignant Hematology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Catherine C Coombs
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aline Renneville
- Laboratory of Hematology, Biology and Pathology Center, CHRU of Lille, Lille, France
| | - Olivier Kosmider
- Laboratory of Hematology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Thorsten Braun
- Department of Hematology, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Uwe Platzbecker
- Department of Hematology and Oncology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Lise Willems
- Department of Hematology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lionel Adès
- Department of Hematology, St Louis Hospital, Assistance Publique-Hôpitaux de Paris, University Paris Diderot, Paris, France
| | - Michaela Fontenay
- Laboratory of Hematology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Raajit Rampal
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Padron
- Malignant Hematology Department, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Nathalie Droin
- INSERM U1170, Gustave Roussy Cancer Center, Villejuif, France
| | - Claude Preudhomme
- Laboratory of Hematology, Biology and Pathology Center, CHRU of Lille, Lille, France
| | - Valeria Santini
- MDS Unit-Hematology, Università di Firenze AOU careggi, Firenze, Italy
| | | | - Pierre Fenaux
- Department of Hematology, St Louis Hospital, Assistance Publique-Hôpitaux de Paris, University Paris Diderot, Paris, France
| | - Eric Solary
- INSERM U1170, Gustave Roussy Cancer Center, Villejuif, France; Department of Hematology, Gustave Roussy Cancer Center, University Paris Sud, Villejuif, France
| | - Raphael Itzykson
- Department of Hematology, St Louis Hospital, Assistance Publique-Hôpitaux de Paris, University Paris Diderot, Paris, France; INSERM/CNRS UMR 944/7212, Saint-Louis Institute, Paris, France.
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14
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Germ line tissues for optimal detection of somatic variants in myelodysplastic syndromes. Blood 2018; 131:2402-2405. [PMID: 29661788 DOI: 10.1182/blood-2018-01-827881] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
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15
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Pogosova-Agadjanyan EL, Moseley A, Othus M, Appelbaum FR, Chauncey TR, Chen IML, Erba HP, Godwin JE, Fang M, Kopecky KJ, List AF, Pogosov GL, Radich JP, Willman CL, Wood BL, Meshinchi S, Stirewalt DL. Impact of Specimen Heterogeneity on Biomarkers in Repository Samples from Patients with Acute Myeloid Leukemia: A SWOG Report. Biopreserv Biobank 2017; 16:42-52. [PMID: 29172682 DOI: 10.1089/bio.2017.0079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Current prognostic models for acute myeloid leukemia (AML) are inconsistent at predicting clinical outcomes for individual patients. Variability in the quality of specimens utilized for biomarker discovery and validation may contribute to this prognostic inconsistency. METHODS We evaluated the impact of sample heterogeneity on prognostic biomarkers and methods to mitigate any adverse effects of this heterogeneity in 240 cryopreserved bone marrow and peripheral blood specimens from AML patients enrolled on SWOG (Southwest Oncology Group) trials. RESULTS Cryopreserved samples displayed a broad range in viability (37% with viabilities ≤60%) and nonleukemic cell contamination (13% with lymphocyte percentages >20%). Specimen viability was impacted by transport time, AML immunophenotype, and, potentially, patients' age. The viability and cellular heterogeneity in unsorted samples significantly altered biomarker results. Enriching for viable AML blasts improved the RNA quality from specimens with poor viability and refined results for both DNA and RNA biomarkers. For example, FLT3-ITD allelic ratio, which is currently utilized to risk-stratify AML patients, was on average 1.49-fold higher in the viable AML blasts than in the unsorted specimens. CONCLUSION To our knowledge, this is the first study to provide evidence that using cryopreserved specimens can introduce uncontrollable variables that may impact biomarker results and enrichment for viable AML blasts may mitigate this impact.
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Affiliation(s)
| | - Anna Moseley
- 2 SWOG Statistical Center , Fred Hutch, Seattle, Washington
| | - Megan Othus
- 2 SWOG Statistical Center , Fred Hutch, Seattle, Washington
| | - Frederick R Appelbaum
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
| | - Thomas R Chauncey
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington.,4 VA Puget Sound Health Care System , Seattle, Washington
| | - I-Ming L Chen
- 5 Department of Pathology, University of New Mexico , UNM Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Harry P Erba
- 6 Division of Hematology and Oncology, University of Alabama at Birmingham , Birmingham, Alabama
| | - John E Godwin
- 7 Providence Cancer Center, Earle A. Chiles Research Institute , Portland, Oregon
| | - Min Fang
- 8 Departments of Laboratory Medicine and Pathology, University of Washington , Seattle, Washington
| | | | - Alan F List
- 9 Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute , Tampa, Florida
| | | | - Jerald P Radich
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
| | - Cheryl L Willman
- 5 Department of Pathology, University of New Mexico , UNM Comprehensive Cancer Center, Albuquerque, New Mexico
| | - Brent L Wood
- 8 Departments of Laboratory Medicine and Pathology, University of Washington , Seattle, Washington
| | - Soheil Meshinchi
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,10 Department of Pediatrics, University of Washington , Seattle, Washington
| | - Derek L Stirewalt
- 1 Clinical Research Division , Fred Hutch, Seattle, Washington.,3 Departments of Oncology and Hematology, University of Washington , Seattle, Washington
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16
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Qu X, Othus M, Davison J, Wu Y, Yan L, Meshinchi S, Ostronoff F, Estey EH, Radich JP, Erba HP, Appelbaum FR, Fang M. Prognostic methylation markers for overall survival in cytogenetically normal patients with acute myeloid leukemia treated on SWOG trials. Cancer 2017; 123:2472-2481. [PMID: 28222251 DOI: 10.1002/cncr.30626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Aberrant DNA methylation is known to occur in patients with acute myeloid leukemia (AML), whereas methylation signatures and prognostic markers have been proposed. The objective of the current study was to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in patients with AML with normal karyotype (AML-NK). METHODS AML-NK samples from 7 SWOG trials were analyzed using a novel genome-wide approach called "CHARMcox" (comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazards model) controlling for known clinical covariates. CHARMcox was applied to a phase 1 discovery cohort (72 patients) to identify survival-associated methylation regions (SAMRs). Subsequently, using bisulfite pyrosequencing, SAMRs were studied in phase 2 model-building (65 patients) and phase 3 validation (65 patients) cohorts. An independent external cohort from The Cancer Genome Atlas (TCGA) AML study (LAML) was used for further validation (93 patients). RESULTS Two SAMRs, located at the CpG island shores of leucine zipper tumor suppressor 2 (LZTS2) and nuclear receptor subfamily 6 group a member 1 (NR6A1), respectively, were identified. Multivariable analyses demonstrated that hypomethylation of either LZTS2 or NR6A1 was associated with worse overall survival in the SWOG cohort (P<.001). The prognosis was validated in patients with AML-NK from the TCGA-LAML cohort. Methylation values below the median at both markers predicted worse overall survival (SWOG: hazard ratio, 1.89 [P<.001]; and TCGA-LAML: hazard ratio, 2.08 [P=.006]). The C-statistic was 0.71 for both cohorts, and the impact was independent of the Fms-related tyrosine kinase 3 internal tandem duplication (FLT3-ITD) status. CONCLUSIONS The 2 methylation markers, measurable by clinically applicable assays such as bisulfite pyrosequencing, are promising for risk stratification among patients with AML-NK. Cancer 2017;123:2472-81. © 2017 American Cancer Society.
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Affiliation(s)
- Xiaoyu Qu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Megan Othus
- Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon
| | - Jerry Davison
- Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Yu Wu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Fabiana Ostronoff
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington
| | - Jerry P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Harry P Erba
- SWOG Leukemia Committee, Portland, Oregon.,Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon.,Department of Medicine, University of Washington, Seattle, Washington
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington.,SWOG Leukemia Committee, Portland, Oregon.,Department of Pathology, University of Washington, Seattle, Washington
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17
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Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy. Blood 2017; 129:1397-1401. [PMID: 28082444 DOI: 10.1182/blood-2016-10-745273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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18
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Suzuki Y, Tomita A, Nakamura F, Iriyama C, Shirahata-Adachi M, Shimada K, Akashi A, Ishikawa Y, Kaneda N, Kiyoi H. Peripheral blood cell-free DNA is an alternative tumor DNA source reflecting disease status in myelodysplastic syndromes. Cancer Sci 2016; 107:1329-37. [PMID: 27323954 PMCID: PMC5021037 DOI: 10.1111/cas.12994] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/17/2022] Open
Abstract
Genetic alterations in myelodysplastic syndromes (MDS) are critical for pathogenesis. We previously showed that peripheral blood cell-free DNA (PBcfDNA) may be more sensitive for genetic/epigenetic analyses than whole bone marrow (BM) cells and mononuclear cells in peripheral blood (PB). Here we analyzed the detailed features of PBcfDNA and its utility in genetic analyses in MDS. The plasma-PBcfDNA concentration in MDS and related diseases (N = 33) was significantly higher than that in healthy donors (N = 14; P = 0.041) and in International Prognostic Scoring System higher-risk groups than that in lower-risk groups (P = 0.034). The concentration of plasma-/serum-PBcfDNA was significantly correlated with the serum lactate dehydrogenase level (both P < 0.0001) and the blast cell count in PB (P = 0.034 and 0.025, respectively). One nanogram of PBcfDNA was sufficient for one assay of Sanger sequencing using optimized primer sets to amplify approximately 160-bp PCR products. PBcfDNA (approximately 50 ng) can also be utilized for targeted sequencing. Almost all mutations detected in BM-DNA were also detected using corresponding PBcfDNA. Analyses using serially harvested PBcfDNA from an RAEB-2 patient showed that the somatic mutations and a single nucleotide polymorphism that were detected before allogeneic transplantation were undetectable after transplantation, indicating that PBcfDNA likely comes from MDS clones that reflect the disease status. PBcfDNA may be a safer and easier alternative to obtain tumor DNA in MDS.
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Affiliation(s)
- Yasuhiro Suzuki
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akihiro Tomita
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Fumika Nakamura
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Analytical Neurobiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Chisako Iriyama
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mizuho Shirahata-Adachi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuyuki Shimada
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Institute for Adavanced Research, Nagoya University, Nagoya, Japan
| | - Akimi Akashi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Ishikawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Kaneda
- Department of Analytical Neurobiology, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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19
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Gronseth CM, McElhone SE, Storer BE, Kroeger KA, Sandhu V, Fero ML, Appelbaum FR, Estey EH, Fang M. Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia. Cancer 2015; 121:2900-8. [PMID: 26033747 DOI: 10.1002/cncr.29475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/13/2015] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Chromosomal abnormalities are important in the diagnosis and prognosis of patients with acute myeloid leukemia (AML). Genomic microarray techniques detect recurrent copy-neutral loss of heterozygosity (cnLOH) in addition to copy number aberrations. However, the clinical utility has not been fully established. Therefore, in the current study, the authors examined the prognostic impact of acquired cnLOH in patients with AML, including complete remission (CR) rate, duration of CR, and overall survival (OS). METHODS A total of 112 consecutive patients with AML who were undergoing chromosome genomic array testing (CGAT) at the Seattle Cancer Care Alliance were included in the current study. DNA from the bone marrow or blood was analyzed with a microarray platform with both single-nucleotide polymorphism (SNP) probes and non-SNP probes to identify acquired cnLOH. Results were correlated with cytogenetic, molecular, immunophenotypic, and other clinicopathological findings. RESULTS Patients with cnLOH demonstrated a shorter duration of CR (hazard ratio, 1.87; P =.04) and worse OS (HR, 1.82; P = .03). Multivariate analyses confirmed the independent predictive value of cnLOH for early disease recurrence (P =.02). These results largely reflected those in patients with intermediate and unfavorable cytogenetics. Most strikingly, 13q cnLOH was found to demonstrate a 6.64-fold higher rate of disease recurrence (P =.006) and 3.45-fold worse OS (P = .02) and was enriched with the FLT3-ITD (Fms-related tyrosine kinase 3-internal tandem duplication) mutation. CONCLUSIONS CnLOH has important prognostic significance in patients with AML. CGAT can replace imbalance fluorescence in situ hybridization and the authors recommend the routine use of CGAT to detect cnLOH, particularly among patients with intermediate-risk cytogenetics.
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Affiliation(s)
| | - Scott E McElhone
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Barry E Storer
- Clinical Statistics Department, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathleen A Kroeger
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Vicky Sandhu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthew L Fero
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
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20
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Mohamedali AM, Gäken J, Ahmed M, Malik F, Smith AE, Best S, Mian S, Gaymes T, Ireland R, Kulasekararaj AG, Mufti GJ. High concordance of genomic and cytogenetic aberrations between peripheral blood and bone marrow in myelodysplastic syndrome (MDS). Leukemia 2015; 29:1928-38. [DOI: 10.1038/leu.2015.110] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/24/2015] [Accepted: 04/16/2015] [Indexed: 12/12/2022]
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21
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Hughes AEO, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, Eades WC, Elliott K, Heath S, Westervelt P, Ding L, Conrad DF, White BS, Shao J, Link DC, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Walter MJ, Graubert TA. Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet 2014; 10:e1004462. [PMID: 25010716 PMCID: PMC4091781 DOI: 10.1371/journal.pgen.1004462] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 05/13/2014] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions—the population frequency of individual clones, their genetic composition, and their evolutionary relationships—which we set out to test by sequencing individual cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples. Single-cell mutation profiling strongly supported the clonal architecture implied by the analysis of bulk material. In addition, it resolved the clonal assignment of single nucleotide variants that had been initially ambiguous and identified areas of previously unappreciated complexity. Accordingly, we find that many of the key assumptions underlying the analysis of tumor clonality by deep sequencing of unfractionated material are valid. Furthermore, we illustrate a single-cell sequencing strategy for interrogating the clonal relationships among known variants that is cost-effective, scalable, and adaptable to the analysis of both hematopoietic and solid tumors, or any heterogeneous population of cells. Human cancers are genetically diverse populations of cells that evolve over the course of their natural history or in response to the selective pressure of therapy. In theory, it is possible to infer how this variation is structured into related populations of cells based on the frequency of individual mutations in bulk samples, but the accuracy of these models has not been evaluated across a large number of variants in individual cells. Here, we report a strategy for analyzing hundreds of variants within a single cell, and we apply this method to assess models of tumor clonality derived from bulk samples in three cases of leukemia. The data largely support the predicted population structure, though they suggest specific refinements. This type of approach not only illustrates the biological complexity of human cancer, but it also has the potential to inform patient management. That is, precise knowledge of which variants are present in which populations of cells may allow physicians to more effectively target combinations of mutations and predict how patients will respond to therapy.
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Affiliation(s)
- Andrew E. O. Hughes
- Center for Genome Sciences and Systems Biology, Washington University, St. Louis, Missouri, United States of America
| | - Vincent Magrini
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
| | - Ryan Demeter
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
| | - Christopher A. Miller
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
| | - Robert Fulton
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
| | - Lucinda L. Fulton
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
| | - William C. Eades
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
| | - Kevin Elliott
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
| | - Sharon Heath
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
| | - Peter Westervelt
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Li Ding
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
| | - Donald F. Conrad
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri, United States of America
| | - Brian S. White
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
| | - Jin Shao
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Daniel C. Link
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - John F. DiPersio
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Elaine R. Mardis
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
| | - Richard K. Wilson
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Timothy J. Ley
- The Genome Institute, Washington University, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Matthew J. Walter
- Department of Genetics, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
| | - Timothy A. Graubert
- Department of Internal Medicine, Division of Oncology, Washington University, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
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22
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Abstract
The myelodysplastic syndromes (MDS) pose a unique diagnostic challenge for clinicians and pathologists due to the clinicopathologic heterogeneity of the disease and overlapping features with other benign and malignant disorders. Currently, the initial evaluation of a patient with suspected MDS centers around a detailed medical history, review of the peripheral blood and bone marrow by an expert hematopathologist and risk stratification using laboratory results, morphology and cytogenetics. More sophisticated technologies, including multi-color flow cytometry, fluorescence in-situ hybridization (FISH), next-generation sequencing, and others are emerging and promise to offer significant refinements in diagnostic, prognostic and, hopefully, therapeutic information. With the incidence and prevalence of MDS increasing worldwide, it is critical for clinicians to optimize the initial evaluation of a patient with suspected disease, using a standard schema, to facilitate accurate diagnosis, risk stratification and treatment.
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23
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Zhao X, Yang F, Li S, Liu M, Ying S, Jia X, Wang X. CpG island methylator phenotype of myelodysplastic syndrome identified through genome-wide profiling of DNA methylation and gene expression. Br J Haematol 2014; 165:649-58. [PMID: 24601943 DOI: 10.1111/bjh.12811] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
Abstract
The CpG island methylator phenotype (CIMP) is an epigenetic phenomenon and plays an important role in tumourigenesis in various cancers. The identification of aberrant DNA methylation can be exploited for early diagnosis and risk assessment of patients. We identified a CIMP in myelodysplastic syndrome (MDS). Genes were screened for hypermethylation and transcription downregulation through genome-wide DNA methylation profiling and gene expression microarrays. Methylation-specific, real-time, and bisulfite-sequencing polymerase chain reaction were performed to validate selected genes. The hypermethylation of genes as a diagnostic tool for the detection of MDS was evaluated. Kaplan-Meier survival analysis and Cox regression were performed. A draft of an MDS CIMP was established and revised to 6 genes after validation in 20 patients and 20 controls. Further large-scale analysis showed that the majority of 211 MDS patients were hypermethylated in 6 genes. The area under the curve of CIMP was 0·9768 (95% confidence interval 0·9609-0·9928). A combination of 5 or more of the methylated genes showed a specificity of 95% and sensitivity of 91% for the diagnosis of MDS. We found CIMP positivity to be a significantly unfavourable prognostic factor for MDS. These results indicate that the newly established CIMP may improve diagnostic accuracy and prognosis assessment in MDS.
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Affiliation(s)
- Xiaoli Zhao
- Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
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24
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Nybakken GE, Bagg A. The genetic basis and expanding role of molecular analysis in the diagnosis, prognosis, and therapeutic design for myelodysplastic syndromes. J Mol Diagn 2014; 16:145-58. [PMID: 24457119 DOI: 10.1016/j.jmoldx.2013.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 11/09/2013] [Accepted: 11/21/2013] [Indexed: 12/31/2022] Open
Abstract
The myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell disorders of ineffective hematopoiesis that characteristically demonstrate peripheral blood cytopenia, bone marrow hypercellularity, and morphologically defined dysplasia of one or more hematopoietic lineages. Classical metaphase cytogenetics and judicious use of fluorescence in situ hybridization play central roles in the contemporary diagnosis and classification of MDS. An abundance of recent molecular studies are beginning to delineate additional genetic and epigenetic aberrations associated with these disorders. These alterations affect diagnosis, prognosis, and therapy, and with this understanding classification systems are evolving from a primarily hematological and morphological basis toward a multifactorial appreciation that includes histomorphology, metaphase cytogenetics, and directed molecular studies. In the present health-care environment, it is critical to develop a cost-effective, efficient testing strategy that maximizes the diagnostic potential of even limited specimens. Here, we briefly review the classical genetic approach to MDS, outline exciting new advances in the molecular understanding of this heterogeneous group of hematological neoplasms, and discuss how these advances are driving the evolution of classification and prognostic systems. Rapidly growing understanding of the genetic basis of MDS holds much promise for testing, and here we provide a frame of reference for discussion of current testing protocols and for addressing testing modalities likely to enter clinical practice in the near future.
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Affiliation(s)
- Grant E Nybakken
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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25
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Itzykson R, Kosmider O, Fenaux P. Somatic mutations and epigenetic abnormalities in myelodysplastic syndromes. Best Pract Res Clin Haematol 2014; 26:355-64. [PMID: 24507812 DOI: 10.1016/j.beha.2014.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During many years, very limited data had been available on specific gene mutations in MDS in particular due to the fact that balanced chromosomal translocations (which have allowed to discover many "leukemia" genes) are very rare in MDS, while chromosomal deletions are generally very large, making it difficult to identify genes of interest. Recently, the advent of next generation sequencing (NGS) techniques has helped identify somatic gene mutations in 75-80% of MDS, that cluster mainly in four functional groups, i.e. cytokine signaling (RAS genes), DNA methylation, (TET2, IDH1/2, DNMT3a genes) histone modifications (ASXL1 and EZH2 genes), and spliceosome (SF3B1 and SRSF2 genes) along with mutations of RUNX1 and TP 53 genes. Most of those mutations, except SF3B1 and TET2 mutations, are associated with an overall poorer prognosis, while some gene mutations (mainly TET2 mutation), may be associated to better response to hypomethylating agents. The frequent mutations of epigenetic modulators in MDS appear to largely contribute to the importance of epigenetic deregulation (in particular gene hypermethylation and histone deacetylation) in MDS progression, and may account at least partially for the efficacy of hypomethylating agents in the treatment of MDS.
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Affiliation(s)
- Raphael Itzykson
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM Unit U944, Hôpital St Louis, Paris, France
| | - Olivier Kosmider
- Laboratoire d'hématologie, Hôpital Cochin, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 5, France
| | - Pierre Fenaux
- Hematology Department, Hôpital Saint-Louis, Assistance Publique - Hôpitaux de Paris (AP-HP), France; Université Paris 7, France; INSERM UMR-S-940, Hôpital St Louis, Paris, France.
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26
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Arenillas L, Mallo M, Ramos F, Guinta K, Barragán E, Lumbreras E, Larráyoz MJ, De Paz R, Tormo M, Abáigar M, Pedro C, Cervera J, Such E, José Calasanz M, Díez-Campelo M, Sanz GF, Hernández JM, Luño E, Saumell S, Maciejewski J, Florensa L, Solé F. Single nucleotide polymorphism array karyotyping: A diagnostic and prognostic tool in myelodysplastic syndromes with unsuccessful conventional cytogenetic testing. Genes Chromosomes Cancer 2013; 52:1167-77. [DOI: 10.1002/gcc.22112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 12/15/2022] Open
Affiliation(s)
- Leonor Arenillas
- Laboratori de CitologiaHematològica. Laboratori de Citogenètica Molecular, Pathology Department, Hospital del Mar, GRETNHE, IMIM (Hospital del Mar ResearchInstitute); Barcelona Spain
| | - Mar Mallo
- Institut de Recerca contra la Leucèmia Josep Carreras (IJC); Badalona Spain
| | - Fernando Ramos
- Hematology Department, Hospital Universitario de León, Instituto de Biomedicina (IBIOMED); Universidad de León; León Spain
| | - Kathryn Guinta
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic; Cleveland OH
| | - Eva Barragán
- Hematology Department; Hospital Universitario La Fe; Valencia Spain
| | - Eva Lumbreras
- IBSAL, IBMCC (Centro de Investigación del Cáncer; Universidad de Salamanca-CSIC) and Hematology Department, Hospital Universitario de Salamanca; Spain
| | | | - Raquel De Paz
- Hematology Department; Hospital Universitario La Paz; Madrid Spain
| | - Mar Tormo
- Hematology and Oncology Department; Hospital Clínico Universitario de Valencia; Spain
| | - María Abáigar
- IBSAL, IBMCC (Centro de Investigación del Cáncer; Universidad de Salamanca-CSIC) and Hematology Department, Hospital Universitario de Salamanca; Spain
| | - Carme Pedro
- Clinic Hematology Department, Hospital del Mar, GRETNHE. IMIM (Hospital del Mar ResearchInstitute); Barcelona Spain
| | - José Cervera
- Hematology Department; Hospital Universitario La Fe; Valencia Spain
| | - Esperanza Such
- Hematology Department; Hospital Universitario La Fe; Valencia Spain
| | | | - María Díez-Campelo
- IBSAL, IBMCC (Centro de Investigación del Cáncer; Universidad de Salamanca-CSIC) and Hematology Department, Hospital Universitario de Salamanca; Spain
| | | | - Jesús María Hernández
- IBSAL, IBMCC (Centro de Investigación del Cáncer; Universidad de Salamanca-CSIC) and Hematology Department, Hospital Universitario de Salamanca; Spain
| | - Elisa Luño
- Hematology Department; Hospital Universitario Central de Asturias; Oviedo Spain
| | - Sílvia Saumell
- Laboratori de CitologiaHematològica. Laboratori de Citogenètica Molecular, Pathology Department, Hospital del Mar, GRETNHE, IMIM (Hospital del Mar ResearchInstitute); Barcelona Spain
| | - Jaroslaw Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic; Cleveland OH
| | - Lourdes Florensa
- Laboratori de CitologiaHematològica. Laboratori de Citogenètica Molecular, Pathology Department, Hospital del Mar, GRETNHE, IMIM (Hospital del Mar ResearchInstitute); Barcelona Spain
| | - Francesc Solé
- Institut de Recerca contra la Leucèmia Josep Carreras (IJC); Badalona Spain
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27
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Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood 2013; 122:3616-27; quiz 3699. [PMID: 24030381 DOI: 10.1182/blood-2013-08-518886] [Citation(s) in RCA: 1382] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of chronic hematological malignancies characterized by dysplasia, ineffective hematopoiesis and a variable risk of progression to acute myeloid leukemia. Sequencing of MDS genomes has identified mutations in genes implicated in RNA splicing, DNA modification, chromatin regulation, and cell signaling. We sequenced 111 genes across 738 patients with MDS or closely related neoplasms (including chronic myelomonocytic leukemia and MDS-myeloproliferative neoplasms) to explore the role of acquired mutations in MDS biology and clinical phenotype. Seventy-eight percent of patients had 1 or more oncogenic mutations. We identify complex patterns of pairwise association between genes, indicative of epistatic interactions involving components of the spliceosome machinery and epigenetic modifiers. Coupled with inferences on subclonal mutations, these data suggest a hypothesis of genetic "predestination," in which early driver mutations, typically affecting genes involved in RNA splicing, dictate future trajectories of disease evolution with distinct clinical phenotypes. Driver mutations had equivalent prognostic significance, whether clonal or subclonal, and leukemia-free survival deteriorated steadily as numbers of driver mutations increased. Thus, analysis of oncogenic mutations in large, well-characterized cohorts of patients illustrates the interconnections between the cancer genome and disease biology, with considerable potential for clinical application.
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